Some Jedi refused to accept their new military status and left the Order, while others still chose to work undercover rather than on the battlefield. Many of the Jedi officers died during the war against the Separatists, and clone troopers killed most of the remaining generals when Order 66 was executed by Supreme ChancellorPalpatine, a Sith Lord.

Unlike the Clone Wars Generals, Jedi who served as commanders in the New Republic and Galactic Alliance forces were generally serving members of those Governments' military arms, often with long decades of professional experience behind them.